search

metaOmics / MetaQC

Apache License 2.0
0 stars 1 forks source link

How to prepare "colLabel" &" "GList" files in package MetaQC? #1

Open mzcs7 opened 5 years ago

mzcs7 commented 5 years ago

I have prepared "DList" file as the instruction of package preproc, however, there is very few information about another two parameters in MetaQC, "colLabel" and "GList". Q1, does "cloLabel mean sample groups? I have noticed the example in data prostate8, whose colLabels are all 0 or 1. Q2, how to load GSEA file into R? I know the "GList" file is obtained from GSEA, but obviously, there are some other steps to shape the GSEA file into "GList". Then, how? Thanks!

mzcs7 commented 5 years ago

@matianzhou Hi Charles, (‾◡◝), SOS~

mzcs7 commented 5 years ago

It seems https://rdrr.io/cran/MetaQC/man/MetaQC.html is the former MetaQC version published by DR.Don. According to these detailed parameters description, I have made "GList" file by code gmt=list(GSA.read.gmt("c7.all.v6.2.symbols.gmt")). But I have some puzzles about preparing "colLabel" file. BTW, I want to make a survival analysis.

matianzhou commented 5 years ago

@mzcs7 I already forwarded your questions to the author of the new MetaQC package (@ShuchangLiu ), she might be able to address your issues.

mzcs7 commented 5 years ago

post my codes and error for now,

library(MetaQC)
gmt=list(GSA.read.gmt("c7.all.v6.2.symbols.gmt")) 
GSE_ALL=c(list(GSE_A),list(GSE_B),list(GSE_C))
names(GSE_ALL)=c("GSE_A","GSE_B","GSE_C")
train_QC=MetaQC(DList = GSE_ALL,
                colLabel = label_list,
                GList = gmt[[1]])

ERROR like this,


[1] "Begin IQC"

Error in wilcox.test.default(x = Dstar, y = Dpound, alternative = "greater") :

Not enough (finite) 'x' observations

In addition: Warning messages:

1: In cor(t(DList[[s]])) : standard deviation is zero

2: In cor(t(DList[[s]])) : standard deviation is zero

My "DList" looks like this, image

and "colLabel", image

Last,

sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[10] base     

other attached packages:
 [1] MetaQC_1.0           multtest_2.38.0      GSA_1.03             preproc_1.2-4       
 [5] DMwR_0.4.1           lattice_0.20-38      AnnotationDbi_1.44.0 IRanges_2.16.0      
 [9] S4Vectors_0.20.1     Biobase_2.42.0       BiocGenerics_0.28.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0         compiler_3.5.2     bitops_1.0-6       class_7.3-15      
 [5] xts_0.11-2         tools_3.5.2        rpart_4.1-13       digest_0.6.18     
 [9] bit_1.1-14         RSQLite_2.1.1      memoise_1.1.0      Matrix_1.2-15     
[13] DBI_1.0.0          curl_3.2           yaml_2.2.0         gtools_3.8.1      
[17] caTools_1.17.1.1   bit64_0.9-7        survival_2.43-3    gdata_2.18.0      
[21] TTR_0.23-4         blob_1.1.1         ROCR_1.0-7         MASS_7.3-51.1     
[25] gplots_3.0.1       splines_3.5.2      abind_1.4-5        quantmod_0.4-13   
[29] KernSmooth_2.23-15 zoo_1.8-4
mzcs7 commented 5 years ago

@ShuchangLiu

mzcs7 commented 5 years ago

@matianzhou Hi Charles, I have made samples' survival status, 0 or 1, to be colLabel. But I want to know, is there any requirement for .gmt file's choice?

If I borrow the "pathway" data in package MetaQC example to analyze my own expression data, the AQCg and AQCp values are all zero.

If I download another .gmt file in MSigDB, for example, "c7.all.v6.2.symbols.gmt", I will meet an error like this, 

[1] "Begin IQC"
    GSE364   GSE10140   GSE15654 
  4.002438 410.000000   2.672635 
[1] "End IQC"
[1] "Begin EQC"
[1] "Warning: EQC to be updated using some temporary values"
[1] "End EQC"
[1] "Begin AQCg"
  GSE364 GSE10140 GSE15654 
       0        0        0 
[1] "End AQCg"
[1] "Begin AQCp"
Error in getAQCp(DList, colLabel, GList, overlapGenes, filterGenes, cutRatioByMean,  : 
  Error: Insufficient number of qualified pathways.

There is limited information in Google about MetaQC, I really feel very puzzled. Maybe I miss something? Could you do me a favor?

Thank you in advance!

matianzhou commented 5 years ago

Did you ask the package author of MetaQC Silvia Liu (cc'ed in the email)?

Best, Charles

Tianzhou (Charles) Ma, PhD Assistant Professor Department of Epidemiology and Biostatistics University of Maryland School of Public Health 2234M SPH Building #255 4200 Valley Drive College Park, MD 20742 Tel: 301-405-6421 Email: tma0929@umd.edu Website: (Department) https://sph.umd.edu/department/epib/bio/91666 (Personal) https://matianzhou.github.io/

On Mon, Mar 25, 2019 at 9:24 PM mzcs7 notifications@github.com wrote:

@matianzhou https://github.com/matianzhou Hi Charles, I have made samples' survival status, 0 or 1, to be colLabel. But I want to know, is there any requirement for .gmt file's choice?

If I borrow the "pathway" data in package MetaQC example to analyze my own expression data, the AQCg and AQCp values are all zero.

If I download another .gmt file in MSigDB, for example, "c7.all.v6.2.symbols.gmt", I will meet an error like this, [1] "Begin IQC" GSE364 GSE10140 GSE15654 4.002438 410.000000 2.672635 [1] "End IQC" [1] "Begin EQC" [1] "Warning: EQC to be updated using some temporary values" [1] "End EQC" [1] "Begin AQCg" GSE364 GSE10140 GSE15654 0 0 0 [1] "End AQCg" [1] "Begin AQCp" Error in getAQCp(DList, colLabel, GList, overlapGenes, filterGenes, cutRatioByMean, : Error: Insufficient number of qualified pathways.

There is limited information in Google about MetaQC, I really feel very puzzled. Maybe I miss something? Could you do me a favor?

Thank you in advance!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/metaOmics/MetaQC/issues/1#issuecomment-476437737, or mute the thread https://github.com/notifications/unsubscribe-auth/APO6RDRrRZYUU7fST3MSEA6khG8gV_MVks5vaXbNgaJpZM4b-UW1 .